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Correct, those 3 clips are for extra standoffs as Morris indicates. Clip them into the square holes under motherboard mounting holes that don't have a raised standoff on the tray. The white plastic stud is used in the slot on the tray that you have circled along with the raised standoffs. The motherboard should mount with the short flat head coarse thread screws, the others are for mounting drives in the cages and cards in the slots. You should have a lot of hardware left over when you are done.
By the way, that's a micro-ATX motherboard, it looks to me like it has 6 mounting holes, 5 for screws and one for the plastic stud. Looks to me like you will be using two of the clips.
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